The bike trail scene in the city is not great, to say the least. And that's me being nice. It's total shit compared to nearby cities.

The loop around Fort McHenry can be combined with riding past Under Armour for a bit of a tour of Locust Point. Riding around Fort McHenry is almost exactly 1 mile and you often need to be careful due to the large amount of people who utilize the trail on a nice day.

Lake Montebello is a better alternative for a short loop than Fort McHenry. It's quite wide so it handles traffic much, much better.

Jones Falls starting in the Woodberry area and going north to Mt Washington is great. I don't know what your level of fitness is but this northern part of the city has some decent climbs in the Mt Washington and Lake Roland areas. The southern part from Woodberry south to Druid Hill to Penn Station is good. It's a mix of riding on low traffic roads and trails (primarily Druid Hill). South of Penn Station to the Inner Harbor is a way to get north/south but nothing I would choose.

Maryland Ave is also generally efficient way of going north/south (to Penn Station as well) but be careful. There's often a lot of assholes in the bike lane plus cars frequently turn across it. Keep your head on a swivel as you approach intersections.

Gwynns Falls is not heavily utilized and goes through/near some rough areas. I'd suggest saving this for group rides.

Herring Run is so-so. Not great. Not bad. If you're by Montebello it's probably worth checking out once. You probably won't have much of a desire to do it a second time.

The Middle Branch Trail is in kind of rough shape, with some parts in quite rough shape. I would not go out of my way to ride this.